Molecular monitoring of hematopoietic chimerism has become a routine diagnostic approach in patients after allogeneic stem cell transplantation. Chimerism testing permits the documentation and surveillance of engraftment and facilitates early detection of impending graft rejection. In patients transplanted for treatment of malignant hematological disorders, monitoring of chimerism can provide an early indication of incipient disease relapse. The investigation of chimerism has therefore become an indispensable tool for the management of patients during the posttransplant period. Growing use of nonmyeloablative conditioning, which is associated with prolonged duration of mixed hematopoietic chimerism, has further increased the clinical importance of chimerism analysis. At present, the most commonly used technical approaches to the investigation of chimerism include microsatellite analysis by polymerase chain reaction and, in the gender-mismatched transplant setting, fluorescence in situ hybridization analysis of sex chromosomes. The investigation of chimerism within specific leukocyte subsets isolated from peripheral blood or bone marrow samples by flow-sorting or magnetic bead-based techniques provides more specific information on processes underlying the dynamics of donor/ recipient chimerism. Moreover, cell subset-specific analysis permits the assessment of impending complications at a significantly higher sensitivity, thus providing a basis for earlier treatment decisions.